It showed sea turtles and dugongs being butchered and environmentalists say the meat is being traded under the guise of traditional hunting.

Activist Rupert Imhoff spent a fortnight in the Torres Strait, filming the hunting of the turtles and dugongs, both listed as vulnerable to extinction.

He used a secret camera to film scenes of animal cruelty, including the slow death of a sea turtle.

Traditional owners are allowed to hunt dugongs and sea turtles under the Native Title Act.

Environmental activist Rupert Imhoff says if it happened anywhere else in Australia, the hunters would be subject to harsh penalties under animal cruelty laws.

"In Queensland, they can do whatever they want and they can do it freely," he said.

Ms Darling says working with Indigenous communities is the best way to stamp out inhumane hunting practices.

She says her department will also work with community leaders to stamp out the practice.

"The actual hunting of these animals can not be prosecuted under animal cruelty laws and that is exactly why we are working with traditional owners up and down the coast of Queensland to make sure these animals are taken in a humane way," she said.

Ms Darling says the investigation will now try to determine whether hunters are complying with the law.

"The export or commercial sale is very concerning and that's what we'll investigate," she said.

Ms Darling says allegations of illegal trade have been made in the past, mostly without any real evidence.

She says it is disappointing the ABC and those involved in last night's report did not provide details to authorities.

Long-held concerns

However, the RSPCA says it has long-held concerns about the way some Indigenous hunters are killing dugongs and sea turtles.

RSPCA spokesman Michael Beatty says authorities will have to embark on a long-term plan to tackle the problem.

"Unfortunately this isn't going to be solved overnight and it involves working with the leaders from the various communities and basically getting them on-side," he said.

"For the most part, the leaders of those communities are on-side already and they want to fix the problem, if you like."

Mr Beatty says the long-standing practices can be changed.

"We're certainly discussing with Aboriginal leaders from various communities about the accessibility of refrigeration and also the way the animals are killed," he said.

"Obviously there's alternatives now so that the animal basically dies instantly and doesn't die a prolonged death."